Class: SampleProcessingProtocol

A sample processing protocol: the recipe, not an execution of it. This is the single home for protocol_url and protocol_version anywhere in sample processing; no SampleProcessing subclass stores them directly. Type-level, so many runs and many samples reference the same record. For "which steps actually ran together", see SampleProcessingRun.

URI: basalt_schema:SampleProcessingProtocol

 classDiagram
    class SampleProcessingProtocol
    click SampleProcessingProtocol href "../SampleProcessingProtocol/"
      SampleProcessingProtocol : description

      SampleProcessingProtocol : id

      SampleProcessingProtocol : name

      SampleProcessingProtocol : protocol_url

      SampleProcessingProtocol : protocol_version

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 String	Human-readable name for the entity or activity	direct
description	0..1 String	Human-readable description for the entity or activity	direct
protocol_url	0..1 String	URL pointing to the protocol used in the activity, if applicable	direct
protocol_version	0..1 String	Version of the protocol used in the activity, if applicable	direct
id	1 Uuid		direct

Usages

used by	used in	type	used
SampleProcessing	in_protocol	range	SampleProcessingProtocol
MediaPreparation	in_protocol	range	SampleProcessingProtocol
CultureGrowth	in_protocol	range	SampleProcessingProtocol
StrainPurity	in_protocol	range	SampleProcessingProtocol
StockCulturePreparation	in_protocol	range	SampleProcessingProtocol
PreCultureGrowth	in_protocol	range	SampleProcessingProtocol
ExperimentalCulture	in_protocol	range	SampleProcessingProtocol
PlateSetupActivity	in_protocol	range	SampleProcessingProtocol
AMP2PlateSetupActivity	in_protocol	range	SampleProcessingProtocol
EcoplatePlateSetupActivity	in_protocol	range	SampleProcessingProtocol
StandardSampleProcessing	in_protocol	range	SampleProcessingProtocol
ChemicalConversionProcess	in_protocol	range	SampleProcessingProtocol
Extraction	in_protocol	range	SampleProcessingProtocol
FiltrationProcess	in_protocol	range	SampleProcessingProtocol
FractionationProcess	in_protocol	range	SampleProcessingProtocol
NormalizationProcess	in_protocol	range	SampleProcessingProtocol
PoolingProcess	in_protocol	range	SampleProcessingProtocol
ProteinQuantification	in_protocol	range	SampleProcessingProtocol
ResuspensionProcess	in_protocol	range	SampleProcessingProtocol
SolidPhaseExtractionProcess	in_protocol	range	SampleProcessingProtocol
SubsamplingProcess	in_protocol	range	SampleProcessingProtocol

Identifier and Mapping Information

Schema Source

from schema: https://emsl-computing.github.io/BASALT-Schema

Mappings

Mapping Type	Mapped Value
self	basalt_schema:SampleProcessingProtocol
native	basalt_schema:SampleProcessingProtocol

LinkML Source

Direct

name: SampleProcessingProtocol
description: 'A sample processing protocol: the recipe, not an execution of it. This
  is the single home for protocol_url and protocol_version anywhere in sample processing;
  no SampleProcessing subclass stores them directly. Type-level, so many runs and
  many samples reference the same record. For "which steps actually ran together",
  see SampleProcessingRun.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
slots:
- name
- description
- protocol_url
- protocol_version
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    identifier: true
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MobilePhase
    - MobilePhaseSubstance
    - CalibrationStandardRun
    - PurchasedMaterial
    - MAOMProduct
    - WEOMProduct
    - organism
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - SubstancesUsedLink
    - SampleProcessingSubstance
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true

Induced

name: SampleProcessingProtocol
description: 'A sample processing protocol: the recipe, not an execution of it. This
  is the single home for protocol_url and protocol_version anywhere in sample processing;
  no SampleProcessing subclass stores them directly. Type-level, so many runs and
  many samples reference the same record. For "which steps actually ran together",
  see SampleProcessingRun.'
from_schema: https://emsl-computing.github.io/BASALT-Schema
attributes:
  id:
    name: id
    from_schema: https://emsl-computing.github.io/BASALT-Schema/sample-processing
    identifier: true
    alias: id
    owner: SampleProcessingProtocol
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MobilePhase
    - MobilePhaseSubstance
    - CalibrationStandardRun
    - PurchasedMaterial
    - MAOMProduct
    - WEOMProduct
    - organism
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - SubstancesUsedLink
    - SampleProcessingSubstance
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true
  name:
    name: name
    description: Human-readable name for the entity or activity.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: SampleProcessingProtocol
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - Study
    - SoftwareControlledTermValue
    range: string
    required: true
  description:
    name: description
    description: Human-readable description for the entity or activity
    title: description
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: SampleProcessingProtocol
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - SampleProcessing
    - Configuration
    - CalibrationStandardRun
    - PurchasedMaterial
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - SampleProcessingProtocol
    - SampleProcessingRun
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
  protocol_url:
    name: protocol_url
    description: URL pointing to the protocol used in the activity, if applicable.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_url
    owner: SampleProcessingProtocol
    domain_of:
    - DataGenerationActivity
    - SampleProcessingProtocol
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol used in the activity, if applicable.
    from_schema: https://emsl-computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_version
    owner: SampleProcessingProtocol
    domain_of:
    - DataGenerationActivity
    - SampleProcessingProtocol
    range: string